Dependency on the splicing factor PHF5A as novel therapeutic target for treatment of pediatric rhabdomyosarcoma

• Applicant: Dr. Sebastian Balbach
• Subject Area: Pediatric and Adolescent Medicine ; Hematology, Oncology
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 493521005

Rhabdomyosarcoma (RMS) is the most common type of soft tissue sarcoma in children and adolescents and remains an unsolved problem of pediatric oncology. Using a CRISPR-Cas9 screen, we identified a strong dependence of RMS cells on PHF5A (PHD finger-like domain-containing protein 5A), which is involved in mRNA processing and splicing. Knockdown of PHF5A using RNA interference and a PHF5A small molecule inhibitor strongly reduced RMS cell viability, validating the result of our screen. Transcriptome profiling by RNA sequencing of RMS cells showed that PHF5A loss induced a dramatic effect on RNA splicing in hundreds of genes, while other genes remained unaffected. Bioinformatic analyses indicate that PHF5A is particularly required for the splicing of transcripts with introns with non-canonical branchpoints, and that PHF5A loss interferes particularly with the expression of certain oncogenic signatures. We therefore hypothesize that PHF5A dependence is a vulnerability of certain cancers and is a potential target for therapy. The proposed project aims to map pre-mRNA binding of PHF5A to understand the molecular mechanism of PHF5A dependence in RMS cells and to highlight the key regulatory circuits interrupted by PHF5A loss of function in rhabdomyosarcoma and potentially other cancers. Ultimately, to pave the way to clinical translation of this novel treatment strategy, we want to evaluate the suitability of PHF5A as target for therapy of cancer in a proof-of-concept study using patient-derived xenograft models.

• DFG Programme: Research Grants